TANK prevents IFN-dependent fatal diffuse alveolar hemorrhage by suppressing DNA-cGAS aggregation

Diffuse alveolar hemorrhage (DAH) is one of the serious complications associated with systemic lupus erythematosus, an autoimmune disease whose pathogenesis involves type I IFNs and cytokines. Here, we show that TANK, a negative regulator of the NF-κB signaling via suppression of TRAF6 ubiquitination, is critical for the amelioration of fatal DAH caused by lung vascular endothelial cell death in a mouse model of systemic lupus erythematosus. The development of fatal DAH in the absence of TANK is mediated by type I IFN signaling, but not IL-6. We further uncover that STING, an adaptor essential for the signaling of cytoplasmic DNA sensor cyclic GMP-AMP (cGAMP) synthase (cGAS), plays a critical role in DAH under Tank deficiency. TANK controls cGAS-mediated cGAMP production and suppresses DNA-mediated induction of IFN-stimulated genes in macrophages by inhibiting the formation of DNA-cGAS aggregates containing ubiquitin. Collectively, TANK inhibits the cGAS-dependent recognition of cytoplasmic DNA to prevent fatal DAH in the murine lupus model.

Protective Roles of Folic Acid in the Responses of Bovine Mammary Epithelial Cells to Different Virulent Staphylococcus aureus Strains

Mastitis caused by Staphylococcus aureus (S. aureus) infection is one of the most difficult diseases to treat in dairy cattle. Exploring the biological progression of S. aureus mastitis via the interaction between host, pathogen, and environment is the key to an effective and sustainable improvement of animal health. Here, two strains of S. aureus and a strain of MRSA (Methicillin-resistant Staphylococcus aureus) isolated from cows with different inflammation phenotypes were used to challenge Mac-T cells and to investigate their effects on the global transcriptome of the cells, then to explore the potential regulatory mechanisms of folic acid on S. aureus mastitis prevention. Differential gene expression or splicing analysis showed that different strains of S. aureus led to distinct transcriptional responses from the host immune system. Folic acid could protect host defense against the challenge of S. aureus and MRSA partially through activating cytoplasmic DNA sensing and tight junction pathway. ZBP1 at the upstream of cytoplasmic DNA sensing pathway was verified and related to anti-pathogen through RNA interference. Further enrichment analysis using these transcriptome data with cattle large-scale genome-wide association study (GWAS) data confirmed that ZBP1 gene is highly associated with bovine somatic cell score (SCS) trait. Our data shed light on the potential effect of FA through regulating key gene and then protect host cells’ defense against S. aureus and MRSA.

A rare moss Cynodontium suecicum (Rhabdoweisiaceae, Bryophyta) on the Barents Sea coast of the Kola Peninsula: morphological and molecular study

Specimens of the rare species Cynodontium suecicum (Rhabdoweisiaceae, Bryophyta) were collected near Drozdovka Bay on the Barents Sea coast of the Kola Peninsula (Russia) in 2016. They were compared with samples of C. suecicum from the Teriberka area (also the coast of the Barents Sea) gathered in 1977 by R. N. Schljakov. The morphological features of both groups of samples were studied, and nucleotide sequence data for ITS1-2 nrDNA and trnL-F cpDNA were obtained. Molecular analysis suggested C. suecicum as a hybrid that inherited cytoplasmic DNA from C. tenellum and nuclear DNA from Kiaeria blyttii. Taking into account the rather clear morphological delimitation against other species, combined with the stability of genetic characters, we believe that S. suecicum should be retained as a species-level taxon.

WY14643 Increases Herpesvirus Replication Independent of PPARα Expression and Inhibits IFNβ Production

Peroxisome proliferator activated receptor (PPAR) agonists are commonly used to treat metabolic disorders in humans because they regulate fatty acid oxidation and cholesterol metabolism. In addition to their roles in controlling metabolism, PPAR agonists also regulate inflammation and are immunosuppressive in models of autoimmunity. We aimed to test whether activation of PPARα with clinically relevant ligands could impact herpesvirus infection using the model strain murine gammaherpesvirus-68. We found that PPARα agonists WY14643 and fenofibrate increased herpesvirus replication in vitro. In vivo, WY14643 increased viral replication and caused lethality in mice. Unexpectedly, these effects proved independent of PPARα. Investigating the mechanism of action for WY14643, we found that it suppresses production of type I interferon by inhibiting stimulator of interferon (STING), which lies downstream of the cytoplasmic DNA sensor cGAS. Thus, WY14643 regulates interferon downstream of cytoplasmic DNA recognition and increases herpesvirus replication in a PPARα-independent manner. Taken together, our data indicate that caution should be employed when using PPARα agonists in immuno-metabolic studies, as they can have off-target effects on viral replication.

Vaccinia E5 is a major inhibitor of the DNA sensor cGAS

The DNA sensor cyclic GMP-AMP synthase (cGAS) is critical in host antiviral immunity. Vaccinia virus (VACV) is a large cytoplasmic DNA virus that belongs to the poxvirus family. How vaccinia virus antagonizes the cGAS-mediated cytosolic DNA-sensing pathway is largely unknown. In this study, we screened 82 vaccinia viral genes to identify potential viral inhibitors of the cGAS/Stimulator of interferon gene (STING) pathway. We discovered that vaccinia E5 is a virulence factor and a major inhibitor of cGAS that elicits proteasome-dependent cGAS degradation. E5 localizes to the cytoplasm and nuclei of infected cells. Cytosolic E5 triggers K48-linked ubiquitination of cGAS and proteasome-dependent degradation via interacting with cGAS. E5 itself also undergoes ubiquitination and degradation. Deleting the E5R gene from the Modified vaccinia virus Ankara (MVA) genome strongly induces type I IFN production by dendritic cells (DCs) and promotes DC maturation, thereby improving the immunogenicity of the viral vector.

A magnet to draw a bright needle out from the haystack -- RADOrgMiner, an automated pipeline to genotype organellar reads from RADseq data

Different versions of Restriction-site Associated DNA sequencing (RADseq) have become powerful and popular tools in molecular ecology. Although RADseq datasets are regarded as representative of the nuclear genome, reduced representation genomic libraries may also sample the organellar (mitochondrial and, in case of plants, plastid) DNA. Extraction of organellar loci from RADseq data can provide additional insights into the phylogenetics of the study group which comes at no additional sequencing effort. Cytoplasmic genetic variance can help better understand the evolutionary history by uncovering past hybridization and identifying the maternal (or, rarely, the paternal) lineage due to rapid lineage sorting. We developed a pipeline in bash that is based on existing bioinformatic tools to automatically mine and genotype organellar loci contained RADseq libraries. The utility of our pipeline is tested on eight, publicly available datasets spanning different phylogenetic levels (i.e. from family-level phylogenies to phylogeography) and RADseq methods (sdRAD, ddRAD, ezRAD, GBS) for genotyping both mitochondrial and plastid loci, which were subject to phylogenetic tree reconstruction. In all cases, organellar phylogenies adequately supplemented the original studies either by corroborating the large-scale picture based on RADseq or by bringing additional evidence on past or contemporary hybridization. RADseq methods designed to achieve a larger horizontal coverage (i.e. ddRAD, ezRAD) evidently yielded longer organellar alignments, but sdRAD and GBS still provided useful polymorphic loci found in the cytoplasmic DNA. Our newly developed pipeline for the above purpose can be run under a Unix-line operating system and is freely accessible at https://github.com/laczkol/RADOrgMiner

STING Signaling and Sterile Inflammation

Innate immunity is regulated by a broad set of evolutionary conserved receptors to finely probe the local environment and maintain host integrity. Besides pathogen recognition through conserved motifs, several of these receptors also sense aberrant or misplaced self-molecules as a sign of perturbed homeostasis. Among them, self-nucleic acid sensing by the cyclic GMP-AMP synthase (cGAS)/stimulator of interferon genes (STING) pathway alerts on the presence of both exogenous and endogenous DNA in the cytoplasm. We review recent literature demonstrating that self-nucleic acid detection through the STING pathway is central to numerous processes, from cell physiology to sterile injury, auto-immunity and cancer. We address the role of STING in autoimmune diseases linked to dysfunctional DNAse or related to mutations in DNA sensing pathways. We expose the role of the cGAS/STING pathway in inflammatory diseases, neurodegenerative conditions and cancer. Connections between STING in various cell processes including autophagy and cell death are developed. Finally, we review proposed mechanisms to explain the sources of cytoplasmic DNA.

A magnet to draw a bright needle out from the haystack -- RADOrgMiner, an automated pipeline to genotype organellar reads from RADseq data

Different versions of Restriction-site Associated DNA sequencing (RADseq) have become powerful and popular tools in molecular ecology. Although RADseq datasets are regarded as representative of the nuclear genome, reduced representation genomic libraries may also sample the organellar (mitochondrial and, in case of plants, plastid) DNA. Extraction of organellar loci from RADseq data can provide additional insights into the phylogenetics of the study group which comes at no additional sequencing effort. Cytoplasmic genetic variance can help better understand the evolutionary history by uncovering past hybridization and identifying the maternal (or, rarely, the paternal) lineage due to rapid lineage sorting. We developed a pipeline in bash that is based on existing bioinformatic tools to automatically mine and genotype organellar loci contained RADseq libraries. The utility of our pipeline is tested on eight, publicly available datasets spanning different phylogenetic levels (i.e. from family-level phylogenies to phylogeography) and RADseq methods (sdRAD, ddRAD, ezRAD, GBS) for genotyping both mitochondrial and plastid loci, which were subject to phylogenetic tree reconstruction. In all cases, organellar phylogenies adequately supplemented the original studies either by corroborating the large-scale picture based on RADseq or by bringing additional evidence on past or contemporary hybridization. RADseq methods designed to achieve a larger horizontal coverage (i.e. ddRAD, ezRAD) evidently yielded longer organellar alignments, but sdRAD and GBS still provided useful polymorphic loci found in the cytoplasmic DNA. Our newly developed pipeline for the above purpose can be run under a Unix-line operating system and is freely accessible at https://github.com/laczkol/RADOrgMiner